package modeling;


/**
 * @author Mathieu Rousseau
 * @email mathieu.rousseau3@mail.mcgill.ca
 */


/** ------------------------------------------------------------------------------------------------------------------
 * start of NormalizationGeneDesertMain class
 * ------------------------------------------------------------------------------------------------------------------  **/
public class NormalizationGeneDesertMain {


	/*  start of main method  */
	public static void main(String[] args){
		
		

		//  parameters for the NormalizationGeneDesert program
		String filenameConditionOne, filenameConditionTwo, filenameBackground;
		
		
		
		//  NormalizationGeneDesert program object
		NormalizationGeneDesert normalizer = new NormalizationGeneDesert();
		
		
		
		
		
		
		
		
		
		/** ------------------------------------------------------------------------------------------------------------------
		 * 
		 * 
		 * 								HARDCODING OF PARAMETERS
		 * 
		 * 
		 * ------------------------------------------------------------------------------------------------------------------  */
		
		
		
		
		//  Condition One is the reference condition
		filenameConditionOne = "DMSO_GDGD.txt";
		
		//  Condition Two is the condition that is being normalized to the reference condition
		//  It is Condition Two that will need to be multiplied by the calculated normalization factor
		filenameConditionTwo = "PMA_GDGD.txt";
		
		//  Background is generally the BAC experiment that is used to calculate the IF values for both of the conditions
		filenameBackground = "BAC_GDGD.txt";
		
		
		
		
		
		/** ------------------------------------------------------------------------------------------------------------------
		 * 
		 * 
		 * 								END OF HARDCODING OF PARAMETERS
		 * 
		 * 
		 * ------------------------------------------------------------------------------------------------------------------  */
		
		
		
		
		
		
		
		
		
		
		//  add all of the parameters to the arguments array
		args = new String[3];
		args[0] = filenameConditionOne;
		args[1] = filenameConditionTwo;
		args[2] = filenameBackground;

		
		//  run the NormalizationGeneDesert program
		normalizer.run(args);
		
		
		
	}/*  end of main method  */

	
	
	
	
}/*  end of NormalizationGeneDesertMain class  */
